Hi Mike,

  I see your test file contains Cu1 and Chimera shows that in a label as CU1 with all upper case.  That surprises me.  Our expert on that Eric Pettersen can explain it next week.  You may be right that Chimera knows the atomic elements and could selectively capitalize labels according to your preferences when the atom name matches the element symbol.  Again it is something Eric can advise on.

     Tom


Tom,

Thanks for the reply.

The file is a PDB, a file with the first few lines is attached.

I was hoping that since Chimera understood atom names well enough to color them that there would be a file with atoms names used for labeling.

If this is something I can change in my installation, great, if not, no worries. I use a mac. I've already changes the python file to understand the non-sttandard space group P21/N.



Cheers,
Mike

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Dr. Michael W. Day
Director - X-ray Crystallography Lab & Molecular Observatory
California Institute of Technology
Mail Code 139-74
Pasadena, CA 91125

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On Feb 11, 2011, at 2:27 PM, Tom Goddard wrote:

Hi Mike,

  Does the FE1 name come from a PDB or Mol2 file you opened?  If that name appears in the file, one obvious approach is to change the file replacing FE1 with Fe1.  I'm not sure if that will break code that expects FE1.  I don't think there are any options in Chimera to manipulate the case of names displayed in labels.  I believe Chimera just uses the capitalization of names it obtains from the file it read in.

  I guess Chimera could have some option to manipulate the case of atom names in labels.  But it seems very specialized.  Someone looking at a protein with a C-alpha atom named CA generally does not want Ca.  This also indicates that it isn't possible to know if an atom name refers to an atomic element (e.g. Fe = iron, Ca = calcium) or something else (like C-alpha).

    Tom

How do I make the default label for metal atoms be upper and lower case?

For instance in an iron compound, if I issue label ~H from the command line the result will be FE1 where I prefer Fe1, etc., etc.

This is true for all two letter atom names.

Thanks
Cheers,
Mike

<<< ------------------------------------------------------------------------>>>
Dr. Michael W. Day
Director - X-ray Crystallography Lab & Molecular Observatory
California Institute of Technology
Mail Code 139-74
Pasadena, CA 91125

<>< <>< <>< <>< <>< <>< <>< <>< <>< <><

Beckman Institute, Room 116
Phone: (626) 395-2734
Fax: (626) 449-4159
<<< ------------------------------------------------------------------------>>>